.command.sh - Workdir - DAQ:GERMLINE_CNV:CalcPanelCoverage (Sig_18_tissue)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/ff94a69b034bfaec20e9322cd216f7/.command.sh
Size: 318 bytes
Task: DAQ:GERMLINE_CNV:CalcPanelCoverage (Sig_18_tissue)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p Sig_18_tissue/
cnv_pipe calc-panel-coverage \
        Sig_18_tissue.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/Sig_18_tissue_counts.tsv \
        4 \
        20 \
        $(pwd)/Sig_18_tissue/